change parameter name

kingaa · Feb 12, 2024 · 3fd533c · 3fd533c
1 parent fe93472
commit 3fd533c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.10.1.5
-Date: 2024-01-27
+Version: 0.10.2.0
+Date: 2024-02-12
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))
 	  )

diff --git a/R/seir.R b/R/seir.R
@@ -10,7 +10,7 @@
 ##' @param sigma progression rate
 ##' @param gamma recovery rate
 ##' @param psi per capita sampling rate
-##' @param delta rate of waning of immunity
+##' @param omega rate of waning of immunity
 ##' @param S0 initial size of susceptible population
 ##' @param E0 initial size of exposed population
 ##' @param I0 initial size of infected population
@@ -26,9 +26,9 @@ NULL
 ##' @export
 runSEIR <- function (
   time, t0 = 0,
-  Beta = 4, sigma = 1, gamma = 1, psi = 1, delta = 0, S0 = 100, E0 = 5, I0 = 5, R0 = 0
+  Beta = 4, sigma = 1, gamma = 1, psi = 1, omega = 0, S0 = 100, E0 = 5, I0 = 5, R0 = 0
 ) {
-  params <- c(Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,delta=delta)
+  params <- c(Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,omega=omega)
   ivps <- c(S0=S0,E0=E0,I0=I0,R0=R0)
   if (any(ivps < 0))
     pStop(paste(sQuote(names(ivps)),collapse=","),
@@ -43,10 +43,10 @@ runSEIR <- function (
 ##' @export
 continueSEIR <- function (
   object, time,
-  Beta = NA, sigma = NA, gamma = NA, psi = NA, delta = NA
+  Beta = NA, sigma = NA, gamma = NA, psi = NA, omega = NA
 ) {
   params <- c(
-    Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,delta=delta
+    Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,omega=omega
   )
   x <- .Call(P_reviveSEIR,object,params)
   .Call(P_runSEIR,x,time) |>
@@ -63,7 +63,7 @@ continueSEIR <- function (
 ##' @export
 seirs_pomp <- function (
   x,
-  Beta, sigma, gamma, psi, delta = 0,
+  Beta, sigma, gamma, psi, omega = 0,
   S0, E0, I0, R0
 )
 {
@@ -84,7 +84,7 @@ seirs_pomp <- function (
     t0=dat$time[1L],
     times=dat$time[-1L],
     params=c(
-      Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,delta=delta,
+      Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,omega=omega,
       ic,N=sum(ic)
     ),
     nstatevars=nsample+8L,
@@ -95,7 +95,7 @@ seirs_pomp <- function (
     dmeasure="seirs_dmeas",
     statenames=c("S","E","I","R","ll","node","linE","linI","lineage"),
     paramnames=c(
-      "Beta","sigma","gamma","psi","delta",
+      "Beta","sigma","gamma","psi","omega",
       "S0","E0","I0","R0","N"
     ),
     PACKAGE="phylopomp"

diff --git a/R/si2r.R b/R/si2r.R
@@ -11,7 +11,7 @@
 ##' @param Beta transmission rate
 ##' @param mu mean superspreading-event cluster size
 ##' @param gamma recovery rate
-##' @param delta rate of waning of immunity
+##' @param omega rate of waning of immunity
 ##' @param psi1,psi2 sampling rates for demes 1 and 2, respectively
 ##' @param sigma12,sigma21 movement rates from deme 1 to 2 and 2 to 1, respectively
 ##' @param S0 initial size of susceptible population
@@ -37,13 +37,13 @@ NULL
 ##' @export
 runSI2R <- function (
   time, t0 = 0,
-  Beta = 5, mu = 5, gamma = 1, delta = 0,
+  Beta = 5, mu = 5, gamma = 1, omega = 0,
   psi1 = 1, psi2 = 0,
   sigma12 = 1, sigma21 = 3,
   S0 = 500, I0 = 10, R0 = 0
 ) {
   params <- c(
-    Beta=Beta,mu=mu,gamma=gamma,delta=delta,
+    Beta=Beta,mu=mu,gamma=gamma,omega=omega,
     psi1=psi1,psi2=psi2,
     sigma12=sigma12,sigma21=sigma21
   )
@@ -58,12 +58,12 @@ runSI2R <- function (
 ##' @export
 continueSI2R <- function (
   object, time,
-  Beta = NA, mu = NA, gamma = NA, delta = NA,
+  Beta = NA, mu = NA, gamma = NA, omega = NA,
   psi1 = NA, psi2 = NA,
   sigma12 = NA, sigma21 = NA
 ) {
   params <- c(
-    Beta=Beta,mu=mu,gamma=gamma,delta=delta,
+    Beta=Beta,mu=mu,gamma=gamma,omega=omega,
     psi1=psi1,psi2=psi2,
     sigma12=sigma12,sigma21=sigma21
   )

diff --git a/R/siir.R b/R/siir.R
@@ -13,7 +13,7 @@
 ##' @param gamma recovery rate.
 ##' @param psi1,psi2 sampling rates.
 ##' @param sigma12,sigma21 movement rates from deme 1 to 2 and 2 to 1, respectively
-##' @param delta rate of loss of immunity
+##' @param omega rate of loss of immunity
 ##' @param S0 initial size of susceptible population.
 ##' @param I1_0 initial size of I2 population.
 ##' @param I2_0 initial size of I2 population.
@@ -31,10 +31,10 @@ runSIIR <- function (
   Beta1 = 5, Beta2 = 5, gamma = 1,
   psi1 = 1, psi2 = 0,
   sigma12 = 0, sigma21 = 0,
-  delta = 0,
+  omega = 0,
   S0 = 500, I1_0 = 10, I2_0 = 10, R0 = 0
 ) {
-  params <- c(Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,delta=delta)
+  params <- c(Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,omega=omega)
   ivps <- c(S0=S0,I1_0=I1_0,I2_0=I2_0,R0=R0)
   x <- .Call(P_makeSIIR,params,ivps,t0)
   .Call(P_runSIIR,x,time) |>
@@ -48,10 +48,10 @@ continueSIIR <- function (
   Beta1 = NA, Beta2 = NA, gamma = NA,
   psi1 = NA, psi2 = NA,
   sigma12 = NA, sigma21 = NA,
-  delta = NA
+  omega = NA
 ) {
   params <- c(
-    Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,delta=delta
+    Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,omega=omega
   )
   x <- .Call(P_reviveSIIR,object,params)
   .Call(P_runSIIR,x,time) |>

diff --git a/R/sir.R b/R/sir.R
@@ -9,7 +9,7 @@
 ##' @param Beta transmission rate.
 ##' @param gamma recovery rate.
 ##' @param psi sampling rate.
-##' @param delta immunity waning rate
+##' @param omega immunity waning rate
 ##' @param S0 initial size of susceptible population.
 ##' @param I0 initial size of infected population.
 ##' @param R0 initial size of recovered population.
@@ -24,10 +24,10 @@ NULL
 ##' @export
 runSIR <- function (
   time,  t0 = 0,
-  Beta = 2, gamma = 1, psi = 1, delta = 0,
+  Beta = 2, gamma = 1, psi = 1, omega = 0,
   S0 = 100, I0 = 2, R0 = 0
 ) {
-  params <- c(Beta=Beta,gamma=gamma,psi=psi,delta=delta)
+  params <- c(Beta=Beta,gamma=gamma,psi=psi,omega=omega)
   ivps <- c(S0=S0,I0=I0,R0=R0)
   if (any(ivps < 0))
     pStop(paste(sQuote(names(ivps)),collapse=","),
@@ -45,9 +45,9 @@ runSIRS <- runSIR
 ##' @inheritParams simulate
 ##' @export
 continueSIR <- function (
-  object, time, Beta = NA, gamma = NA, psi = NA, delta = NA
+  object, time, Beta = NA, gamma = NA, psi = NA, omega = NA
 ) {
-  params <- c(Beta=Beta,gamma=gamma,psi=psi,delta=delta)
+  params <- c(Beta=Beta,gamma=gamma,psi=psi,omega=omega)
   x <- .Call(P_reviveSIR,object,params)
   .Call(P_runSIR,x,time) |>
     structure(model="SIR",class=c("gpsim","gpgen"))
@@ -61,7 +61,7 @@ continueSIR <- function (
 ##' \code{sir_pomp} constructs a \pkg{pomp} object containing a given set of data and a SIR model.
 ##' @importFrom pomp pomp onestep covariate_table
 ##' @export
-sir_pomp <- function (x, Beta, gamma, psi, delta = 0, S0, I0, R0, t0=0)
+sir_pomp <- function (x, Beta, gamma, psi, omega = 0, S0, I0, R0, t0=0)
 {
   ic <- as.integer(c(S0,I0,R0))
   names(ic) <- c("S0","I0","R0")
@@ -74,7 +74,7 @@ sir_pomp <- function (x, Beta, gamma, psi, delta = 0, S0, I0, R0, t0=0)
   pomp(
     data=NULL,
     times=dat$time[-1L],t0=t0,
-    params=c(Beta=Beta,gamma=gamma,psi=psi,delta=delta,ic,N=sum(ic)),
+    params=c(Beta=Beta,gamma=gamma,psi=psi,omega=omega,ic,N=sum(ic)),
     covar=covariate_table(
       dat,
       times="time",
@@ -84,7 +84,7 @@ sir_pomp <- function (x, Beta, gamma, psi, delta = 0, S0, I0, R0, t0=0)
     rprocess=onestep("sirs_gill"),
     dmeasure="sirs_dmeas",
     statenames=c("S","I","R","ll"),
-    paramnames=c("Beta","gamma","psi","delta","S0","I0","R0","N"),
+    paramnames=c("Beta","gamma","psi","omega","S0","I0","R0","N"),
     covarnames=c("lineages","code"),
     PACKAGE="phylopomp"
   )

diff --git a/examples/movie.R b/examples/movie.R
@@ -8,7 +8,7 @@
   )
 
   pb <- utils::txtProgressBar(0,length(times),0,style=3)
-  x <- simulate("SIIR",time=0,Beta1=5,Beta2=10,gamma=1,delta=0.5,
+  x <- simulate("SIIR",time=0,Beta1=5,Beta2=10,gamma=1,omega=0.5,
     psi1=0.2,psi2=0.1,sigma12=1,sigma21=1,S0=200,I1_0=3,I2_0=2)
   for (k in seq_len(length(times))) {
     x <- simulate(x,time=times[k])

diff --git a/examples/seir.R b/examples/seir.R
@@ -9,8 +9,8 @@ runSEIR(Beta=3,gamma=0.1,psi=0.2,S0=100,I0=5,R0=0,time=2,t0=0) -> x
 plot_grid(plotlist=list(plot(x,points=TRUE),diagram(x)),
   ncol=1,rel_heights=c(4,1))
 
-simulate("SEIR",sigma=1,delta=1,time=20,I0=4) |> plot(obscure=FALSE)
+simulate("SEIR",sigma=1,omega=1,time=20,I0=4) |> plot(obscure=FALSE)
 
-simulate("SEIR",sigma=1,delta=1,time=20,I0=4) |>
+simulate("SEIR",sigma=1,omega=1,time=20,I0=4) |>
   lineages(obscure=FALSE) |>
   plot()
diff --git a/examples/si2r.R b/examples/si2r.R
@@ -12,7 +12,7 @@ simulate("SI2R",time=5) |>
 simulate("SI2R",time=2) |>
   diagram(m=30)
 
-simulate("SI2R",time=20,delta=0.2,mu=20) -> x
+simulate("SI2R",time=20,omega=0.2,mu=20) -> x
 plot_grid(
   x |> plot(obscure=FALSE),
   x |> lineages(obscure=FALSE) |> plot(),

diff --git a/examples/sir.R b/examples/sir.R
@@ -9,5 +9,5 @@ runSIR(Beta=3,gamma=0.1,psi=0.2,S0=100,I0=5,R0=0,time=2,t0=0) -> x
 plot_grid(plotlist=list(plot(x,points=TRUE),diagram(x)),
   ncol=1,rel_heights=c(4,1))
 
-simulate("SIRS",delta=1,time=20,I0=4) |> plot()
-simulate("SIRS",delta=1,time=20,I0=4) |> lineages() |> plot()
+simulate("SIRS",omega=1,time=20,I0=4) |> plot()
+simulate("SIRS",omega=1,time=20,I0=4) |> lineages() |> plot()
diff --git a/man/seir.Rd b/man/seir.Rd
diff --git a/man/si2r.Rd b/man/si2r.Rd
diff --git a/man/siir.Rd b/man/siir.Rd